5-36624000-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004172.5(SLC1A3):​c.182-5450G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,048 control chromosomes in the GnomAD database, including 32,274 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 32274 hom., cov: 32)

Consequence

SLC1A3
NM_004172.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.574
Variant links:
Genes affected
SLC1A3 (HGNC:10941): (solute carrier family 1 member 3) This gene encodes a member of a member of a high affinity glutamate transporter family. This gene functions in the termination of excitatory neurotransmission in central nervous system. Mutations are associated with episodic ataxia, Type 6. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC1A3NM_004172.5 linkc.182-5450G>C intron_variant ENST00000265113.9 NP_004163.3 P43003-1A0A024R050Q8N169

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC1A3ENST00000265113.9 linkc.182-5450G>C intron_variant 1 NM_004172.5 ENSP00000265113.4 P43003-1

Frequencies

GnomAD3 genomes
AF:
0.649
AC:
98575
AN:
151930
Hom.:
32245
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.575
Gnomad AMI
AF:
0.629
Gnomad AMR
AF:
0.715
Gnomad ASJ
AF:
0.698
Gnomad EAS
AF:
0.686
Gnomad SAS
AF:
0.724
Gnomad FIN
AF:
0.716
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.657
Gnomad OTH
AF:
0.685
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.649
AC:
98660
AN:
152048
Hom.:
32274
Cov.:
32
AF XY:
0.654
AC XY:
48626
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.576
Gnomad4 AMR
AF:
0.715
Gnomad4 ASJ
AF:
0.698
Gnomad4 EAS
AF:
0.685
Gnomad4 SAS
AF:
0.724
Gnomad4 FIN
AF:
0.716
Gnomad4 NFE
AF:
0.657
Gnomad4 OTH
AF:
0.684
Alfa
AF:
0.638
Hom.:
3699
Bravo
AF:
0.647
Asia WGS
AF:
0.730
AC:
2534
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
CADD
Benign
1.9
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10941306; hg19: chr5-36624102; API